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<center><b>
 [ <a href="module-tree.html">Module Hierarchy</a>
 | <a href="class-tree.html">Class Hierarchy</a> ]
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<h1 class="epydoc">Class Hierarchy</h1>
<ul class="nomargin-top">
    <li> <strong class="uidlink">object</strong>:
      <em class="summary">The most base type</em>
    <ul>
    <li> <strong class="uidlink"><i>unreachable</i>.Object</strong>
    <ul>
    <li> <strong class="uidlink">PySide.QtCore.QObject</strong>
    <ul>
    <li> <strong class="uidlink">PySide.QtCore.QCoreApplication</strong>
    <ul>
    <li> <strong class="uidlink">PySide.QtGui.QApplication</strong>
    <ul>
    <li> <strong class="uidlink"><a href="moltk.gui.moltk_app.MoltkApp-class.html">moltk.gui.moltk_app.MoltkApp</a></strong>
    </li>
    </ul>
    </li>
    </ul>
    </li>
    <li> <strong class="uidlink">PySide.QtGui.QWidget</strong>
    <ul>
    <li> <strong class="uidlink">PySide.QtOpenGL.QGLWidget</strong>
    <ul>
    <li> <strong class="uidlink"><a href="moltk.gui.structure_canvas.StructureCanvas-class.html">moltk.gui.structure_canvas.StructureCanvas</a></strong>:
      <em class="summary">Widget for displaying 3D molecule structure in the MolTK GUI.</em>
    </li>
    </ul>
    </li>
    <li> <strong class="uidlink">PySide.QtGui.QMainWindow</strong>
    <ul>
    <li> <strong class="uidlink"><a href="moltk.gui.moltk_app.MoltkMainWindow-class.html">moltk.gui.moltk_app.MoltkMainWindow</a></strong>
    </li>
    </ul>
    </li>
    </ul>
    </li>
    <li> <strong class="uidlink"><a href="moltk.gui.structure_renderer.StructureRenderer-class.html">moltk.gui.structure_renderer.StructureRenderer</a></strong>:
      <em class="summary">StructureRenderer is a custom renderer class that performs all 
        OpenGL operations in a separate thread.</em>
    </li>
    </ul>
    </li>
    <li> <strong class="uidlink">PySide.QtGui.QPaintDevice</strong>
    <ul>
    <li> <strong class="uidlink">PySide.QtGui.QWidget</strong>
    <ul>
    <li> <strong class="uidlink">PySide.QtOpenGL.QGLWidget</strong>
    <ul>
    <li> <strong class="uidlink"><a href="moltk.gui.structure_canvas.StructureCanvas-class.html">moltk.gui.structure_canvas.StructureCanvas</a></strong>:
      <em class="summary">Widget for displaying 3D molecule structure in the MolTK GUI.</em>
    </li>
    </ul>
    </li>
    <li> <strong class="uidlink">PySide.QtGui.QMainWindow</strong>
    <ul>
    <li> <strong class="uidlink"><a href="moltk.gui.moltk_app.MoltkMainWindow-class.html">moltk.gui.moltk_app.MoltkMainWindow</a></strong>
    </li>
    </ul>
    </li>
    </ul>
    </li>
    </ul>
    </li>
    </ul>
    </li>
    <li> <strong class="uidlink"><a href="moltk.gui.moltk_ui.Ui_MoltkMainWindow-class.html">moltk.gui.moltk_ui.Ui_MoltkMainWindow</a></strong>
    </li>
    <li> <strong class="uidlink"><i>unreachable</i>.instance</strong>
    <ul>
    <li> <strong class="uidlink"><a href="moltk.Aligner-class.html">moltk.Aligner</a></strong>:
      <em class="summary">The Aligner class creates macromolecule sequence alignments and 
        structure alignments.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Alignment-class.html">moltk.Alignment</a></strong>:
      <em class="summary">Alignment represents a set of aligned macromolecule sequences 
        and/or structures.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Angle-class.html">moltk.Angle</a></strong>:
      <em class="summary">Quantity represents a physical value with a unit, such as 5.6 nanometers</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.AngleDimension-class.html">moltk.AngleDimension</a></strong>:
      <em class="summary">Dimension represents a physical dimension such as mass, length, 
        time, etc.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.PDBStructure.Atom-class.html">moltk.PDBStructure.Atom</a></strong>:
      <em class="summary">Structure::Atom represents a chemical atom in a molecular 
        structure.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.BaseBiosequence-class.html">moltk.BaseBiosequence</a></strong>:
      <em class="summary">Parent class for macromolecule sequences and structures.</em>
    <ul>
    <li> <strong class="uidlink"><a href="moltk.Biosequence-class.html">moltk.Biosequence</a></strong>:
      <em class="summary">A macromolecule sequence (DNA or RNA or protein)</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.PDBStructure.Chain-class.html">moltk.PDBStructure.Chain</a></strong>:
      <em class="summary">Chain represents a single polymer or molecule in a PDBStructure.</em>
    </li>
    </ul>
    </li>
    <li> <strong class="uidlink"><a href="moltk.BaseBiosequence.BaseResidue-class.html">moltk.BaseBiosequence.BaseResidue</a></strong>:
      <em class="summary">Parent class for macromolecule sequence residues (nucleotides or 
        amino acids)</em>
    <ul>
    <li> <strong class="uidlink"><a href="moltk.BiosequenceResidue-class.html">moltk.BiosequenceResidue</a></strong>:
      <em class="summary">One residue in a macromolecule sequence (a nucleotide or amino 
        acid)</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.PDBStructure.Residue-class.html">moltk.PDBStructure.Residue</a></strong>:
      <em class="summary">Residue represents a single amino acid or nucleotide residue, or a 
        small molecule, in a macromolecule structure.</em>
    </li>
    </ul>
    </li>
    <li> <strong class="uidlink"><a href="moltk.BitUnit-class.html">moltk.BitUnit</a></strong>:
      <em class="summary">Unit represents a unit of measure, such as gram, nanometer, or 
        second.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.DPTableILU1-class.html">moltk.DPTableILU1</a></strong>:
      <em class="summary">Generic dynamic programming table (not implemented yet...)</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Displacement-class.html">moltk.Displacement</a></strong>:
      <em class="summary">Vector3D_&lt;&gt; is an arbitrary point or vector in 3-space.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.EString-class.html">moltk.EString</a></strong>:
      <em class="summary">A compact representation of the gapping pattern for one sequence in
        an alignment.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Information-class.html">moltk.Information</a></strong>:
      <em class="summary">Quantity represents a physical value with a unit, such as 5.6 nanometers</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.InformationDimension-class.html">moltk.InformationDimension</a></strong>:
      <em class="summary">Dimension represents a physical dimension such as mass, length, 
        time, etc.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Length-class.html">moltk.Length</a></strong>:
      <em class="summary">Quantity represents a physical value with a unit, such as 5.6 nanometers</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.LengthDimension-class.html">moltk.LengthDimension</a></strong>:
      <em class="summary">Dimension represents a physical dimension such as mass, length, 
        time, etc.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.NanometerUnit-class.html">moltk.NanometerUnit</a></strong>:
      <em class="summary">Unit represents a unit of measure, such as gram, nanometer, or 
        second.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.PDBStructure-class.html">moltk.PDBStructure</a></strong>:
      <em class="summary">PDBStructure represents a macromolecule structure as found in a 
        Protein Data Bank file.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Quaternion-class.html">moltk.Quaternion</a></strong>:
      <em class="summary">Quaternion is an elegant 4-element representation of a 3D rotation.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.RadianUnit-class.html">moltk.RadianUnit</a></strong>:
      <em class="summary">Unit represents a unit of measure, such as gram, nanometer, or 
        second.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.RigidTransform-class.html">moltk.RigidTransform</a></strong>:
      <em class="summary">RigidTransform converts one reference frame to another with 
        rotation and translation.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Rotation3D-class.html">moltk.Rotation3D</a></strong>:
      <em class="summary">Rotation3D represents a rotation matrix.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Rotation3D.Row-class.html">moltk.Rotation3D.Row</a></strong>:
      <em class="summary">One row of three numbers in a Rotation3D rotation matrix.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Alignment.Row-class.html">moltk.Alignment.Row</a></strong>:
      <em class="summary">Meta-data for one sequence in an Alignment</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Aligner.Scorer-class.html">moltk.Aligner.Scorer</a></strong>:
      <em class="summary">Scorer can convert, in O(m+n) time, dumb sequence and structure 
        residues into TargetPositions and QueryPositions, which can 
        efficiently compute alignment scores.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.TableType-class.html">moltk.TableType</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.UnitVector3D-class.html">moltk.UnitVector3D</a></strong>:
      <em class="summary">UnitVector3D represents a direction in 3 space, and, unlike 
        Vector3D_&lt;&gt;, does NOT have Units.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Vector3D-class.html">moltk.Vector3D</a></strong>:
      <em class="summary">Vector3D_&lt;&gt; is an arbitrary point or vector in 3-space.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.EString.const_iterator-class.html">moltk.EString.const_iterator</a></strong>:
      <em class="summary">Iterator for accessing the residue positions encoded in an estring.</em>
    </li>
    <li> <strong class="uidlink"><a href="moltk.std_vector_QueryPositionI1-class.html">moltk.std_vector_QueryPositionI1</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.std_vector_TargetPositionI1-class.html">moltk.std_vector_TargetPositionI1</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.std_vector_int-class.html">moltk.std_vector_int</a></strong>
    </li>
    </ul>
    </li>
    <li> <strong class="uidlink">int</strong>:
      <em class="summary">int(x[, base]) -&gt; integer</em>
    <ul>
    <li> <strong class="uidlink"><a href="PySide.QtGui.QApplication.ColorSpec-class.html">PySide.QtGui.QApplication.ColorSpec</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="PySide.QtGui.QMainWindow.DockOption-class.html">PySide.QtGui.QMainWindow.DockOption</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="PySide.QtGui.QMainWindow.DockOptions-class.html">PySide.QtGui.QMainWindow.DockOptions</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="PySide.QtCore.QCoreApplication.Encoding-class.html">PySide.QtCore.QCoreApplication.Encoding</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="PySide.QtGui.QPaintDevice.PaintDeviceMetric-class.html">PySide.QtGui.QPaintDevice.PaintDeviceMetric</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="PySide.QtGui.QWidget.RenderFlag-class.html">PySide.QtGui.QWidget.RenderFlag</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="PySide.QtGui.QWidget.RenderFlags-class.html">PySide.QtGui.QWidget.RenderFlags</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="PySide.QtGui.QApplication.Type-class.html">PySide.QtGui.QApplication.Type</a></strong>
    </li>
    <li> <strong class="uidlink"><i>unreachable</i>.enum</strong>
    <ul>
    <li> <strong class="uidlink"><a href="moltk.DPAlignGapping-class.html">moltk.DPAlignGapping</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.DPAlignScale-class.html">moltk.DPAlignScale</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.DPMemoryModel-class.html">moltk.DPMemoryModel</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.DimensionIndex-class.html">moltk.DimensionIndex</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Alignment.List-class.html">moltk.Alignment.List</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.PDBStructure.Atom.RecordType-class.html">moltk.PDBStructure.Atom.RecordType</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.Aligner.Stage-class.html">moltk.Aligner.Stage</a></strong>
    </li>
    <li> <strong class="uidlink"><a href="moltk.TracebackPointer-class.html">moltk.TracebackPointer</a></strong>
    </li>
    </ul>
    </li>
    </ul>
    </li>
    </ul>
    </li>
</ul>
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